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Date Created: 09/27/15
Taxonomy and Phylogenies naming taxonomy 39 diagram of evolutionary relatedness phylogeny 39 Being in the same species then genus 39 Clade monophyletic taxon a group of species that includes an ancestral species and all it s descendants monophyletic single 39 paraphyletic leaves some out 39 polyphyletic accidental 39 Phylogenetic Trees like a family tree but MUCH FARTHER BACK IN TIME 39 family tree includes an ancestor and ALL of their descendants 0 phylogeny contains ANCESTRAL species and all DESCENDANTS species 39 Hypothetical Phylogeny branch point node Where lineages diverge 39 mangrove nch and woodpecker nch are sister taxa 39 being in the same genus should mean you have a recent common ancestor than species in different genera Constructing Phylogenetic Trees Using cladistics a method for identifying monophyletic groups clades 39 is a salamander more closely related to a turtle or leopard Answer Neither same relatedness 39 shared derived characters 39 trait found in descendants not common ancestor of the group being studied 39 characters used in cladistics can include DNA sequences 39 Characters used in cladistics can include DNA sequences 39 align sequences reveals differences of how many bases 4 39 GenBank online collection of all publicly available DNA sequences with link to info on the sequence EX protein function 39 blast computer program that nds and aligns DNA your query vs what s in GenBank 39 Uses statistical theory 39 helps determine if the observed similarity is due to ave gotten same mutations 39 by chance analogous 39 common ancestry homologous 39 characters used in cladistics can include DNA sequences 39 Or its products DNA RNA translated into amino acids proteins traits 39 RNA is a nucleic acid compose dog nucleotide base pairs like DNA 39 proteins are chains of amino acids which can analyzed as traits for phylogenetic too Ingroups vs Outgroups 39 species we went to know evolutionary relationships for ingroup 39 group we are confident is less closely related than all species in the ingroup reference point for cladistic analysis outgroup 39 Rooting a tree shows which taxa have a more recent common ancestor 39 Trees are commonly rooted by including an outgroup in the analysis the root is placed between the ingroup and the out group 39 does length of line mean anything 39 only if unit of measure is given 39 otherwise just reveals common ancestry among taxa Molecular Clock 39 fossils can show time since divergence for two taxa 39 number of base pair differences in a gene are measured for the taxa 39 provides an estimate of the rate of change for that gene 39 cladistics uses two approaches maximum likelihood and maximum parsimony 39 two mathematical ways ti choose among alternate phylogenies or at least to narrow the possibilities 39 important because 3 species 3 possible trees 4 species 15 possible trees 8 species 100000 trees 39 equations rules in computer programs are used for both ways of generating and picking trees 39 maximum parsimony assumes tree that requires fewest evolutionary changes appearances of shared derived characters is most likely 39 parsimony idea that simpler hypothesis are preferable to more complicated ones 39 maximum likely hood assumes certain rules about how DNA changes over time 39 IF DNA sequences are used as characters to create a phylogeny how to decide which loci to use 39 1 some genes evolve slowly EX DNA that codes for RNAn Longtime ago 39 2 some genes evolve faster EX 12 per 1 mil yrs Recent 39 3 molecular clocks estimates of sequence differences per time 39 USED FOR fossil records divergence between 2 taxa 3 Domains of Life 39 EUKARYA animals plants fungi protists 39 Archaea thermophiles halophiles methanobacterium 0 Bacteria E Coli Staphylococcus BUT tree or web of life Both Horizontal Gene Transfer movement of genes form one genome to another Eukarya s nuclear DNA EX DNA in mitochondria chloroplasts is closer to Archaea History of Life on Earth 39 Possible pathways for the origin of life how could life have originated by natural processes 39 need to consider conditions on early earth liquid water certain gases volcanoes meteorites OR on another planet 39 Hypothesized steps to initial very simple cells abiotic synthesis of small organic molecules that define life EX nucleotide base pairs amino acids 39 Step 1 abiotic synthesis of small organ molecules 39 lst Miller and Urey 1953 mixed gases thought to have been in earth s early atmosphere simulated lightening with electricity spontaneous synthesis of amino acids 39 Has been shown in labs under multiple possible conditions 39 other energy sources that may have facilitated abiotic synthesis hydrothermal deepsea vents 39 Hypothesized steps to initial very simple cells Step 2 0 joining of these small molecules nucleotide base pairs amino acids 39 DNA RNA Protein macromolecules via polymerization 39 Can happen spontaneously BUT catalyzed EX faster on hot clay sand or rock 39 Hypothesized steps to initial very simple cells Step 3 packing of molecules into protocells Mix of what organic molecules including lipids oil lipid bilayer EX like cell membrane 1 maintain internal chemical 2 exhibit simple reproduction 3 can contain macromolecules 39 lst genetic material was probably RNA 39 Evidence certain RNA molecules can make complementary copies of short stretches of RNA EX short stretches of RNA can selfreplicate 39 RNA can provide a template for DNA RNADNA 39 then why DNA RNA Now 39 molecules that were more stable replicated more quickly would have left the most descendant molecules which is more stable RNA or DNA DNA 39 Oxygen Revolution 39 What s important about an atmosphere with oxygen 39 oxygen attacks some chemical bonds some reactions cannot take place in the presence of oxygen 0 big change in environment 39 strong natural selection 0 many anaerobic organisms could not survive First Eukaryotes Prokaryotes and Eukaryotes both plasma membrane cytoplasm DNA Ribosomes Eukaryotes nuclear envelope membranebound organelles 39 Mitochondria and plastids share characteristics With prokaryotic singlecelled organisms 39 circular DNA 39 homologous 0 membrane proteins 39 similar ribosomes 39 similar reproduction 39 rst eukaryotes endosymbiotic theory 0 Multicellularity may have evolved more than once 0 cells living colonially and cooperatively had advantages 39 specialization took on different roles performed different functions REMEMBER Bacteria and Archaea are PROKARYOTES 39 some bacteria fungi and protists are pathogens 39 plant base of food webs guide drug discovery 39 much biological research relies on model organism 39 YOU 10 trillion human cells and 100 trillion bacterial cells